Data from: Three-dimensional single-cell transcriptome imaging of thick tissues

Multiplexed error-robust fluorescence in-situ hybridization
(MERFISH) allows genome-scale imaging of RNAs in individual cells in
intact tissues. To date, MERFISH has been applied to image thin tissue
samples of ∼10-µm thickness. Here, we present a method to enable
three-dimensional (3D) single-cell transcriptome imaging of thick tissue
specimens by integrating MERFISH with confocal microscopy for optical
sectioning and deep learning to increase imaging speed and quality. We
demonstrated 3D MERFISH on mouse brain tissue sections of up to 200 µm
thickness with high detection efficiency and accuracy. We anticipate that
3D thick-tissue MERFISH imaging will broaden the scope of questions that
can be addressed by spatial genomics.

多重误差校正荧光原位杂交（Multiplexed error-robust fluorescence in-situ hybridization, MERFISH）可在完整组织的单个细胞中实现全基因组规模的RNA成像。迄今为止，MERFISH仅被应用于厚度约10微米的薄组织样本成像。本文报道一种可实现厚组织标本三维（3D）单细胞转录组成像的方法，该方法通过将MERFISH与用于光学切片的共聚焦显微镜及深度学习技术相结合，以提升成像速度与成像质量。我们针对厚度可达200微米的小鼠脑组织切片开展了三维MERFISH成像，实现了高检测效率与准确性。我们预计，三维厚组织MERFISH成像将拓宽空间基因组学可解答的问题范畴。